## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354101.sorted.bam --OUTPUT SRX7354101.markdup.sorted.bam --METRICS_FILE SRX7354101.markdup.sorted.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORTED true --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Homo_sapiens_assembly38_noALT_noHLA_noDecoy_patched_ERCC92.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Oct 27 17:37:48 GMT 2023 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE Unknown Library 129339 30460099 3831397 11590159 104030 13041847 0 0.428959 24457615 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 12531926 12531926 2.0 1.287819 3135758 3135758 3.0 1.370659 851327 851327 4.0 1.394501 299959 299959 5.0 1.401364 146071 146071 6.0 1.403339 89167 89167 7.0 1.403907 60912 60912 8.0 1.404071 44912 44912 9.0 1.404118 34331 34331 10.0 1.404132 27382 27382 11.0 1.404136 22077 22077 12.0 1.404137 18345 18345 13.0 1.404137 15485 15485 14.0 1.404137 13148 13148 15.0 1.404137 11254 11254 16.0 1.404137 9787 9787 17.0 1.404137 8465 8465 18.0 1.404137 7499 7499 19.0 1.404137 6554 6554 20.0 1.404137 5746 5746 21.0 1.404137 5141 5141 22.0 1.404137 4598 4598 23.0 1.404137 4174 4174 24.0 1.404137 3838 3838 25.0 1.404137 3603 3603 26.0 1.404137 3139 3139 27.0 1.404137 2943 2943 28.0 1.404137 2649 2649 29.0 1.404137 2525 2525 30.0 1.404137 2384 2384 31.0 1.404137 2093 2093 32.0 1.404137 1960 1960 33.0 1.404137 1839 1839 34.0 1.404137 1794 1794 35.0 1.404137 1578 1578 36.0 1.404137 1503 1503 37.0 1.404137 1391 1391 38.0 1.404137 1283 1283 39.0 1.404137 1318 1318 40.0 1.404137 1146 1146 41.0 1.404137 1114 1114 42.0 1.404137 1031 1031 43.0 1.404137 952 952 44.0 1.404137 976 976 45.0 1.404137 848 848 46.0 1.404137 835 835 47.0 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